GT: Genotyping Comparison Analysis and Clustering/Heatmap
Created: 2011-09-01 17:52:22
Last updated: 2011-09-10 01:01:04
Creates a genotyping comparison analysis Excel file and heatmap image given final report and gender call input files. User provides a plate number and can choose to either load the data into the database or not (y/n). Note that if user chooses "y" the script will take longer to run.
Before running, make sure the final report and gender call text files are correctly named and that they are in the correct directory under: /gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/Plate_#
Results will be stored under this directory:
/gne/research/data/bioinfo/gcell/genotype/prd/Plate_#
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Workflow Components
![header=[] body=[This is the author information extracted from the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Authors (1)
![header=[] body=[These are the descriptive titles embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Titles (1)
GT: Genotyping Comparison Analysis and Clustering/Heatmap |
![header=[] body=[These are the descriptions embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Descriptions (1)
Creates a genotyping comparison analysis Excel file and heatmap image given final report and gender call input files. User provides a plate number and can choose to either load the data into the database or not (y/n). Note that if user chooses "y" the script will take longer to run.
Before running, make sure the final report and gender call text files are correctly named and that they are in the correct directory under: /gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/Plate_#
Results will be stored under this directory:
/gne/research/data/bioinfo/gcell/genotype/prd/Plate_# |
![header=[] body=[These are the listed dependencies of the workflow] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Dependencies (0)
Processors (13)
Name |
Type |
Description |
genotyping_comparison |
externaltool |
|
clustering |
externaltool |
|
app_dir |
stringconstant |
Value/gne/research/apps/gcell/prd/arch-indep/bin |
Ask |
localworker |
Scriptimport javax.swing.JOptionPane;
answer = JOptionPane.showInputDialog(null, (message == void ? null : message), (title == void ? null : title), JOptionPane.QUESTION_MESSAGE);
|
message_value |
stringconstant |
ValueType in your input values. Make sure they are comma delimited with no spaces in-between: ("New plate" ex: 1 || "Existing plate(s)" ex: 1,3,28 || "CLID(s)" ex: CL12345,CL65432 || "All" leave the input BLANK and press "ok" |
title_value |
stringconstant |
ValueA |
Choose |
localworker |
Scriptimport javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
if ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {
throw new RuntimeException("selectionValues must be specified and non-empty");
}
ButtonGroup group = new ButtonGroup();
JPanel messagePanel = new JPanel();
messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));
messagePanel.add(new JLabel((message == void ? null : message)));
JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];
for (int i = 0; i < buttonArray.length; i++) {
buttonArray[i] = new JRadioButton(selectionValues.get(i));
if (i==0) buttonArray[i].setSelected(true);
group.add(buttonArray[i]);
messagePanel.add(buttonArray[i]);
}
JOptionPane.showOptionDialog(null, messagePanel, (title == void ? null : title),
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null);
String answer="";
for (JRadioButton button : buttonArray) {
if (button.isSelected()) {
answer=button.getText();
}
}
|
Split_string_into_string_list_by_regular_expression |
localworker |
ScriptList split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
|
regex_value |
stringconstant |
Value, |
string_value |
stringconstant |
ValueNew plate (and load to database), New plate (don't load to database),Existing plate(s),CLID(s),All past plates |
message_value_1 |
stringconstant |
ValueChoose an analysis type: |
title_value_1 |
stringconstant |
ValueAnalysis Selection |
Beanshell |
beanshell |
Scriptarg2 = "n";
if (type.equals("New plate (and load to database)")) {
arg = "p";
arg2 = "y";
} else if ( type.equals("New plate (don't load to database)")) {
} else if (type.equals("Existing plate(s)")) {
arg = "e";
} else if (type.equals("CLID(s)")) {
arg = "c";
} else if (type.equals("All past plates")) {
arg = "a";
} else {
arg = "p";
} |
Beanshells (1)
Name |
Description |
Inputs |
Outputs |
Beanshell |
|
type
|
arg
arg2
|
Outputs (3)
Name |
Description |
cluster_status |
|
genotype_status |
|
error_report |
|
Datalinks (19)
Source |
Sink |
app_dir:value |
genotyping_comparison:app_dir |
Beanshell:arg |
genotyping_comparison:arg_type |
Beanshell:arg2 |
genotyping_comparison:db_load |
Ask:answer |
genotyping_comparison:plate_num |
app_dir:value |
clustering:app_dir |
Beanshell:arg |
clustering:arg_type |
Ask:answer |
clustering:plate_num |
message_value:value |
Ask:message |
title_value:value |
Ask:title |
Split_string_into_string_list_by_regular_expression:split |
Choose:selectionValues |
message_value_1:value |
Choose:message |
title_value_1:value |
Choose:title |
regex_value:value |
Split_string_into_string_list_by_regular_expression:regex |
string_value:value |
Split_string_into_string_list_by_regular_expression:string |
Choose:answer |
Beanshell:type |
genotyping_comparison:STDERR |
error_report |
clustering:STDERR |
error_report |
clustering:STDOUT |
cluster_status |
genotyping_comparison:STDOUT |
genotype_status |
Coordinations (1)
Controller |
Target |
Choose |
Ask |
Uploader
License
All versions of this Workflow are
licensed under:
Version 2
(of 7)
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